When I increase my vlc sound more than 100% and after stoping or pausing vlc if I use clementine to play music the volume is same as vlc, i.e, more than 100% but in the indicator it shows whatever the previous set state, is this a bug? if so bug of vlc/clementine/gnome-shelll?

I am unaware of how this works in-depth, but if you adjust the volume in the full-blown sound menu (at least for gnome), you'll find the system volume itself goes over 100%, and VLC adjusts system volume, not it's own (personally, I think it's simpler that way, though if it's a huge deal to you, I'm sure there's an option somewhere to adjust its volume relative to the system)